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Harris started fishing with his father at age eight and after high school began crab fishing. He initially worked on a crab boat as an unpaid deckhand until he proved his worth. By the time he was 21 he was one of the youngest crab fishing boat captains on the Bering Sea. He had been captain of the Cornelia Marie for more than 20 years at the time of his death.

From 2004 and until his death, Harris and his boat were followed by an embedded film crew for the series Deadliest Catch. The Cornelia Marie was first shown during the opilio crab portion of Season 1, as partner ship of the F/V Maverick. The "Cornelia Marie" was heavily involved in search efforts for the Big Valley after it sank. It became a regular fixture of the show from the second season on.

Harris was thrown from his bunk during a storm in the 2008 season, and thought he had broken his ribs. He spent several hours coughing up blood until his sons and crew finally convinced him to seek medical attention and enlisted the film crew to watch his condition. Doctors later determined that he had suffered a pulmonary embolism. Medical treatment for this condition prevented him from fishing for almost a year. He returned for the opilio crab fishing season in January 2009.

Some of Harris's sea stories were included in the book Deadliest Catch: Desperate Hours. In 2008, Harris developed a line of coffees, "Captain's Reserve", with blends named after fishing themes such as "Harris Family Blend" and "Midnight Sunrise."[5]

Harris's chain-smoking, which was frequently seen on the show,[6] added to his health woes.

Captain Harris suffered a massive stroke during the sixth televised opilio crab season of Deadliest Catch. He was offloading crab on January 29, 2010 at St. Paul Island, Alaska. He was flown to Anchorage for surgery, and was placed in an induced coma to reduce intracranial pressure and swelling. He awoke from the coma after his condition improved. He was squeezing hands, talking, and showing other signs of improvement.[7] Harris' doctors were amazed by his extreme improvement, saying that he was making gains in a few days that usually take months for stroke victims. However, Harris died from an intracranial hemorrhage on February 9, 2010.

Captain Phil Harris was cremated, and half of the ashes were buried (in an ornately painted Harley Davidson motorcycle gas tank) with the remains of his mother. Harris' family spread the remainder of the ashes at sea.[8]

His sons Jacob and Joshua issued a statement from the Harris family, saying, "It is with great sadness that we say goodbye to our dad -- Captain Phil Harris. Dad has always been a fighter and continued to be until the end. For us and the crew, he was someone who never backed down. We will remember and celebrate that strength. Thanks to everyone for their thoughts and prayers."[9]

The sixth season of Deadliest Catch featured footage of Phil Harris at work for the last time. The series began airing on the Discovery Channel on April 13, 2010. A memorial service to Phil Harris was hosted by the Discovery Channel along Seattle's waterfront on Smith Cove Cruise Terminal at Pier 91 on Friday evening, April 30, 2010. This was the night before the Puget Sound's annual Opening Day for boating season. Phil's sons Jake and Josh Harris spoke at this service. A boat gave a final salute from the location where Phil's vessel is based in Elliott Bay.[10][11][12][13][14][15]

Harris was single at the time of his death, but had been married and divorced twice. His first marriage, from 1982 to 1991 was to Mary Harris, mother of his two sons, Joshua and Jacob. Joshua and Jacob worked on board his fishing vessel, Cornelia Marie, as deckhands. His hometown was Bothell, Washington. He enjoyed driving fast and owned both a Harley-Davidson motorcycle and a Chevrolet Corvette.[16] Besides driving fast and fishing, he also enjoyed building bird feeders.[17]

Before his death, Phil Harris set up a coffee company called the Captain's Reserve. His sons Jake and Joshua are now in the process of promoting the brand and expanding the family business. National retail expansion began January 2011, and went global the same year.[18]